Date: Wed, 24 Nov 2004 16:52:28 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Cc: linimon@FreeBSD.org Subject: ports/74333: update biology/emboss and take maintainership Message-ID: <200411241952.iAOJqSDm075249@pi.iib.unsam.edu.ar> Resent-Message-ID: <200411242000.iAOK0kkL037991@freefall.freebsd.org>
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>Number: 74333 >Category: ports >Synopsis: update biology/emboss and take maintainership >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Wed Nov 24 20:00:46 GMT 2004 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 4.10-RELEASE i386 >Organization: IIB-UNSAM >Environment: FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan@pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI i386 >Description: The EMBOSS port is currently at v2.4.1 and was being maintained by Johann Visagie. Over time, several updates have been submitted. I've taken care of the update to v2.6.0 (ports/48786, now obsolete). Another PR by Choe Cheng-Dae, updating EMBOSS to v2.8.0 is now also obsolete (ports/68950) given that EMBOSS is now at 2.9.0. This patches update EMBOSS to the latest stable release. While here, I have separated the third party contributed stuff (embassy) onto a port of their own (biology/embassy). I'm also asking for adoption of this now orphaned port. >How-To-Repeat: >Fix: --- emboss.diff begins here --- diff -ruN /usr/ports/biology/emboss/Makefile emboss/Makefile --- /usr/ports/biology/emboss/Makefile Mon Nov 22 06:09:09 2004 +++ emboss/Makefile Wed Nov 24 16:04:45 2004 @@ -2,141 +2,56 @@ # Date created: 31 July 2000 # Whom: Johann Visagie <johann@egenetics.com> # -# $FreeBSD: ports/biology/emboss/Makefile,v 1.40 2004/11/20 07:40:43 linimon Exp $ +# $FreeBSD: ports/biology/emboss/Makefile,v 1.39 2004/06/23 08:20:21 vs Exp $ # PORTNAME= emboss -PORTVERSION= 2.4.1 -PORTREVISION= 3 +PORTVERSION= 2.9.0 CATEGORIES= biology -MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/old/ \ - ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/old/ -# ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ +MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ + ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \ + ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ +DISTNAME= ${PORTNAME:U}-${PORTVERSION} DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX} -DIST_SUBDIR= ${PORTNAME} -EXTRACT_ONLY= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX} -MAINTAINER= ports@FreeBSD.org +MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= A collection of open source tools for genetic sequence analysis -LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd +BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw \ + primer3:${PORTSDIR}/biology/primer3 +LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd \ + png.5:${PORTSDIR}/graphics/png USE_SUBMAKE= yes USE_GMAKE= yes GNU_CONFIGURE= yes +USE_LIBTOOL_VER=15 INSTALLS_SHLIB= yes USE_XLIB= yes USE_MOTIF= yes -USE_PERL5_BUILD=yes +USE_REINPLACE= yes PKGMESSAGE= ${WRKDIR}/pkg-message -.if exists(${WRKDIRPREFIX}${.CURDIR}/Makefile.inc) -.include "${WRKDIRPREFIX}${.CURDIR}/Makefile.inc" -.endif - -CONFIGURE_ENV+= CPPFLAGS="-I${LOCALBASE}/include" \ - LIBS="-L${LOCALBASE}/lib -L${X11BASE}/lib" -SCRIPTS_ENV+= WRKDIRPREFIX="${WRKDIRPREFIX}" \ - MKDIR="${MKDIR}" RM="${RM}" - -WRKSRC= ${WRKDIR}/${PORTNAME:U}-${PORTVERSION} -EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY -EMNU_VERSION= 1.0.5 -HMMER_VERSION= 2.1.1 -MEME_VERSION= 2.3.1 -MSE_VERSION= 0.0.4 -TOPO_VERSION= 0.1 -PHYLIP_VERSION= 3.573c DOC_DIRS= doc/manuals doc/tutorials doc/programs/text doc/programs/html CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template -.for app in EMNU HMMER MEME MSE PHYLIP TOPO -SCRIPTS_ENV+= ${app}_VERSION="${${app}_VERSION}" -.if defined(WITH_${app}) -APPLIST+= ${app} -${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION} -${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX} -DISTFILES+= ${${app}_DISTFILE} -PLIST_${app}= "" -.else -PLIST_${app}= "@comment " -.endif -PLIST_SUB+= PLIST_${app}=${PLIST_${app}} -.endfor - -# Jemboss support is a work in progress. -# -#.if defined(WITH_JEMBOSS) -#USE_JAVA= 1.3+ -#CONFIGURE_ARGS+= --with-java=${JAVA_HOME}/include \ -# --with-javaos=${JAVA_HOME}/include/${JAVA_OS:L} -#CONFIGURE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin -#MAKE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin -#JEMBOSS_WRKSRC= ${WRKSRC}/jemboss -#.endif - -pre-fetch: - @ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME} - -post-extract: -.for app in ${APPLIST} - @ ${MKDIR} ${EMBASSY_WRKDIR} - @ cd ${EMBASSY_WRKDIR} && ${EXTRACT_CMD} ${EXTRACT_BEFORE_ARGS} \ - ${_DISTDIR}/${${app}_DISTFILE} ${EXTRACT_AFTER_ARGS} - @ if [ `id -u` = 0 ]; then \ - ${CHMOD} -R ug-s ${${app}_WRKSRC}; \ - ${CHOWN} -R 0:0 ${${app}_WRKSRC}; \ - fi -.endfor - post-patch: +.if !defined(NOPORTDOCS) .for DIR in ${DOC_DIRS} - @ ${PERL} -pi.orig -e \ - 's#\$$\(prefix\)/share/\$$\(PACKAGE\)/doc#\$$\(datadir\)/doc/\$$\(PACKAGE\)#' \ + ${REINPLACE_CMD} -e \ + 's#$$(prefix)/share/$$(PACKAGE)/doc#$$(datadir)/doc/$$(PACKAGE)#' \ ${WRKSRC}/${DIR}/Makefile.in .endfor - -post-configure: -.for app in ${APPLIST} - @ cd ${${app}_WRKSRC} && \ - ${SETENV} CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" \ - CXXFLAGS="${CXXFLAGS}" \ - INSTALL="/usr/bin/install -c -o ${BINOWN} -g ${BINGRP}" \ - INSTALL_DATA="${INSTALL_DATA}" \ - INSTALL_PROGRAM="${INSTALL_PROGRAM}" \ - INSTALL_SCRIPT="${INSTALL_SCRIPT}" \ - ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS} -.endfor - -post-build: -.for app in ${APPLIST} - @ cd ${${app}_WRKSRC} && \ - ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ - ${MAKE_ARGS} -.endfor -#.if defined(WITH_JEMBOSS) -# @ cd ${JEMBOSS_WRKSRC} && \ -# ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ -# ${MAKE_ARGS} -#.endif +.endif post-install: -.for app in ${APPLIST} - @ cd ${${app}_WRKSRC} && \ - ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ - ${MAKE_ARGS} ${INSTALL_TARGET} -.endfor - @ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \ - ${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \ - ${CHOWN} ${SHAREOWN}:${SHAREGRP} \ - ${PREFIX}/etc/emboss.default.sample - @ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \ - pkg-message > ${PKGMESSAGE} + @ cd ${WRKSRC} && \ + ${SED} -e 's#%%PREFIX%%#${PREFIX}#' \ + ${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \ + ${CHOWN} ${SHAREOWN}:${SHAREGRP} ${PREFIX}/etc/emboss.default.sample + @ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE} .if !defined(BATCH) @ ${CAT} ${PKGMESSAGE} .endif - -post-clean: - @ ${RM} -f ${WRKDIRPREFIX}${.CURDIR}/Makefile.inc .include <bsd.port.mk> diff -ruN /usr/ports/biology/emboss/distinfo emboss/distinfo --- /usr/ports/biology/emboss/distinfo Mon Sep 30 16:23:36 2002 +++ emboss/distinfo Thu Nov 4 17:15:33 2004 @@ -1,7 +1,2 @@ -MD5 (emboss/EMBOSS-2.4.1.tar.gz) = f8e8f053362346d45b696ad6d0ec4aad -MD5 (emboss/EMNU-1.0.5.tar.gz) = 6ba42bfd8484b313f39ef81e03141f66 -MD5 (emboss/HMMER-2.1.1.tar.gz) = aff42ea8ced9c049f2cc4f84a10efd21 -MD5 (emboss/MEME-2.3.1.tar.gz) = 92302d22ccb94f9e77c1bb2ca35c0f9c -MD5 (emboss/MSE-0.0.4.tar.gz) = fdfdb7f4d92f67323b14b7030a1135c9 -MD5 (emboss/PHYLIP-3.573c.tar.gz) = 5fa81a3cfb4f502c627a30428d49a084 -MD5 (emboss/TOPO-0.1.tar.gz) = a5131f2e0d58e06ce071250b62cbe65a +MD5 (EMBOSS-2.9.0.tar.gz) = c6facfd1750e88a0c8b7bb7ac826d472 +SIZE (EMBOSS-2.9.0.tar.gz) = 14479274 diff -ruN /usr/ports/biology/emboss/files/patch-aa emboss/files/patch-aa --- /usr/ports/biology/emboss/files/patch-aa Wed Jul 11 10:33:34 2001 +++ emboss/files/patch-aa Wed Dec 31 21:00:00 1969 @@ -1,26 +0,0 @@ -Add ${PREFIX}/etc as an acceptable location for emboss.default. (I'm still -waiting for this to be incorporated into an official release of EMBOSS.) - -The port installs ${PREFIX}/etc/emboss.default.sample - --- Johann <wjv@FreeBSD.org> - - ---- ajax/ajnam.c.orig Thu Aug 17 20:31:30 2000 -+++ ajax/ajnam.c Mon Aug 28 15:12:09 2000 -@@ -984,6 +984,15 @@ - prefixRootFile = fopen (ajStrStr(namRootStr), "r"); - } - -+ /* look for $(PREFIX)_ROOT/../emboss.default */ -+ -+ if (!prefixRootFile) -+ { -+ ajFmtPrintS (&namRootStr, "%s/etc/%s.default", -+ namInstallRoot, prefix); -+ prefixRootFile = fopen (ajStrStr(namRootStr), "r"); -+ } -+ - if (namFileOrig) - (void) ajStrAppC (&namFileOrig, ", "); - (void) ajStrApp (&namFileOrig, namRootStr); diff -ruN /usr/ports/biology/emboss/files/patch-ajax::ajjava.c emboss/files/patch-ajax::ajjava.c --- /usr/ports/biology/emboss/files/patch-ajax::ajjava.c Fri Jul 5 07:09:32 2002 +++ emboss/files/patch-ajax::ajjava.c Wed Dec 31 21:00:00 1969 @@ -1,11 +0,0 @@ ---- ajax/ajjava.c.orig Thu May 2 22:06:08 2002 -+++ ajax/ajjava.c Sun May 26 09:14:20 2002 -@@ -75,7 +75,7 @@ - #endif - - #ifndef __ppc__ --#include <crypt.h> -+#include <unistd.h> - #endif - - diff -ruN /usr/ports/biology/emboss/files/patch-configure emboss/files/patch-configure --- /usr/ports/biology/emboss/files/patch-configure Mon Jan 29 12:48:01 2001 +++ emboss/files/patch-configure Wed Dec 31 21:00:00 1969 @@ -1,11 +0,0 @@ ---- configure.orig Mon Jan 22 23:28:17 2001 -+++ configure Thu Jan 25 19:07:33 2001 -@@ -1473,7 +1473,7 @@ - - - --AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" -+AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\"" - - #AC_PROG_CXX - for ac_prog in mawk gawk nawk awk diff -ruN /usr/ports/biology/emboss/files/patch-emboss-emboss.default.template emboss/files/patch-emboss-emboss.default.template --- /usr/ports/biology/emboss/files/patch-emboss-emboss.default.template Wed May 30 11:34:56 2001 +++ emboss/files/patch-emboss-emboss.default.template Wed Dec 31 21:00:00 1969 @@ -1,38 +0,0 @@ ---- emboss/emboss.default.template.orig Thu May 24 19:36:39 2001 -+++ emboss/emboss.default.template Wed May 30 10:23:48 2001 -@@ -1,9 +1,31 @@ --#SET emboss_tempdata name_of_emboss_test_database_directory -+##################################################### -+### Configuration options for FreeBSD EMBOSS port ### -+##################################################### - --# Logfile - set this to a file that any user can append to --# and EMBOSS applications will automatically write log information -+# The directory where EMBOSS expects to find run-time -+# databases. This is the compiled-in default - change -+# only if you know what you're doing! -+# -+#SET emboss_data %%PREFIX%%/share/EMBOSS/data - --#SET emboss_logfile /packages/emboss/emboss/log -+# This is an alias which is internal to this -+# configuration file and is set here merely as a -+# convenience. It points to the location where you -+# have placed your local databases (this will differ -+# from site to site). -+# -+SET emboss_tempdata %%PREFIX%%/share/EMBOSS/databases -+ -+# Logfile. If this is uncommented and set to a file -+# that any user can append to, EMBOSS applications -+# will automatically log usage information. -+# -+#SET emboss_logfile /var/log/emboss.log -+ -+ -+########################################### -+### Configuration options for databases ### -+########################################### - - # swissprot (Puffer fish entries) - # ========= diff -ruN /usr/ports/biology/emboss/pkg-message emboss/pkg-message --- /usr/ports/biology/emboss/pkg-message Wed Jul 11 10:58:12 2001 +++ emboss/pkg-message Wed Nov 3 18:29:55 2004 @@ -15,7 +15,8 @@ system-wide emboss.default. Online EMBOSS documentation is available at: - http://www.uk.embnet.org/Software/EMBOSS/general.html + http://www.uk.embnet.org/Software/EMBOSS/userdoc.html http://www.uk.embnet.org/Software/EMBOSS/Doc/ + http://emboss.sourceforge.net/docs/ -------------------------------------------------------------------------- diff -ruN /usr/ports/biology/emboss/pkg-plist emboss/pkg-plist --- /usr/ports/biology/emboss/pkg-plist Mon Sep 30 16:23:36 2002 +++ emboss/pkg-plist Wed Nov 24 16:24:36 2004 @@ -1,94 +1,10 @@ -%%PLIST_EMNU%%bin/emnu -%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd -%%PLIST_HMMER%%bin/ealistat -%%PLIST_HMMER%%bin/ehmmalign -%%PLIST_HMMER%%bin/ehmmbuild -%%PLIST_HMMER%%bin/ehmmcalibrate -%%PLIST_HMMER%%bin/ehmmconvert -%%PLIST_HMMER%%bin/ehmmemit -%%PLIST_HMMER%%bin/ehmmfetch -%%PLIST_HMMER%%bin/ehmmindex -%%PLIST_HMMER%%bin/ehmmpfam -%%PLIST_HMMER%%bin/ehmmsearch -%%PLIST_HMMER%%lib/libhmmer.a -%%PLIST_HMMER%%lib/libhmmer.la -%%PLIST_HMMER%%lib/libhmmer.so -%%PLIST_HMMER%%lib/libhmmer.so.2 -%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd -%%PLIST_MEME%%bin/meme -%%PLIST_MEME%%lib/libmeme.a -%%PLIST_MEME%%lib/libmeme.la -%%PLIST_MEME%%lib/libmeme.so -%%PLIST_MEME%%lib/libmeme.so.2 -%%PLIST_MEME%%share/EMBOSS/acd/meme.acd -%%PLIST_MSE%%bin/mse -%%PLIST_MSE%%lib/libckit.a -%%PLIST_MSE%%lib/libckit.la -%%PLIST_MSE%%lib/libckit.so -%%PLIST_MSE%%lib/libckit.so.1 -%%PLIST_MSE%%share/EMBOSS/acd/mse.acd -%%PLIST_PHYLIP%%bin/eclique -%%PLIST_PHYLIP%%bin/econsense -%%PLIST_PHYLIP%%bin/econtml -%%PLIST_PHYLIP%%bin/econtrast -%%PLIST_PHYLIP%%bin/ednacomp -%%PLIST_PHYLIP%%bin/ednadist -%%PLIST_PHYLIP%%bin/ednainvar -%%PLIST_PHYLIP%%bin/ednaml -%%PLIST_PHYLIP%%bin/ednamlk -%%PLIST_PHYLIP%%bin/ednapars -%%PLIST_PHYLIP%%bin/ednapenny -%%PLIST_PHYLIP%%bin/edollop -%%PLIST_PHYLIP%%bin/edolpenny -%%PLIST_PHYLIP%%bin/efactor -%%PLIST_PHYLIP%%bin/efitch -%%PLIST_PHYLIP%%bin/egendist -%%PLIST_PHYLIP%%bin/ekitsch -%%PLIST_PHYLIP%%bin/emix -%%PLIST_PHYLIP%%bin/eneighbor -%%PLIST_PHYLIP%%bin/epenny -%%PLIST_PHYLIP%%bin/eprotdist -%%PLIST_PHYLIP%%bin/eprotpars -%%PLIST_PHYLIP%%bin/erestml -%%PLIST_PHYLIP%%bin/eseqboot -%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd -%%PLIST_TOPO%%bin/topo -%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd +bin/aaindexextract bin/abiview bin/acdc -bin/alignwrap +bin/acdpretty +bin/acdtable +bin/acdtrace +bin/acdvalid bin/antigenic bin/backtranseq bin/banana @@ -104,7 +20,6 @@ bin/coderet bin/compseq bin/cons -bin/contacts bin/cpgplot bin/cpgreport bin/cusp @@ -117,11 +32,9 @@ bin/dbigcg bin/degapseq bin/descseq -bin/dichet bin/diffseq bin/digest bin/distmat -bin/domainer bin/dotmatcher bin/dotpath bin/dottup @@ -132,6 +45,8 @@ bin/emma bin/emowse bin/entret +bin/epestfind +bin/eprimer3 bin/equicktandem bin/est2genome bin/etandem @@ -151,6 +66,7 @@ bin/infoalign bin/infoseq bin/isochore +bin/jembossctl bin/lindna bin/listor bin/marscan @@ -160,14 +76,14 @@ bin/megamerger bin/merger bin/msbar +bin/mwcontam bin/mwfilter bin/needle bin/newcpgreport bin/newcpgseek bin/newseq -bin/noreturn bin/notseq -bin/nrscope +bin/noreturn bin/nthseq bin/octanol bin/oddcomp @@ -195,7 +111,7 @@ bin/prophet bin/prosextract bin/pscan -bin/psiblasts +bin/psiphi bin/rebaseextract bin/recoder bin/redata @@ -203,9 +119,6 @@ bin/restover bin/restrict bin/revseq -bin/runJemboss.csh -bin/scopalign -bin/scope bin/seealso bin/seqmatchall bin/seqret @@ -217,144 +130,670 @@ bin/showseq bin/shuffleseq bin/sigcleave -bin/siggen -bin/sigscan bin/silent +bin/sirna +bin/sixpack +bin/skipseq bin/splitter bin/stretcher bin/stssearch bin/supermatcher -bin/swissparse bin/syco +bin/tcode bin/textsearch bin/tfextract bin/tfm bin/tfscan bin/tmap +bin/tranalign bin/transeq bin/trimest bin/trimseq +bin/twofeat +bin/union bin/vectorstrip bin/water +bin/whichdb bin/wobble bin/wordcount bin/wordmatch bin/wossname +bin/yank +bin/runJemboss.csh etc/emboss.default.sample -lib/libajax.a -lib/libajax.la -lib/libajax.so +include/drivers.h +include/pdf.h +include/plcore.h +include/plevent.h +include/plplotP.h +include/plxwd.h +include/metadefs.h +include/plConfig.h +include/pldebug.h +include/plplot.h +include/plstrm.h +include/plDevs.h +include/ajax.h +include/ajarch.h +include/ajdefine.h +include/ajacd.h +include/ajalign.h +include/ajarr.h +include/ajassert.h +include/ajbase.h +include/ajcall.h +include/ajcod.h +include/ajdan.h +include/ajdmx.h +include/ajdomain.h +include/ajexcept.h +include/ajfeat.h 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+share/EMBOSS/jemboss/resources/filemgr.html +share/EMBOSS/jemboss/resources/seqList.html +share/EMBOSS/jemboss/utils/install-jemboss-server.sh +share/EMBOSS/jemboss/utils/keys.sh +share/EMBOSS/jemboss/utils/makeJar.csh +share/EMBOSS/jemboss/utils/makeJNLP.sh +share/EMBOSS/jemboss/utils/makeFileManagerJNLP.sh +share/EMBOSS/jemboss/utils/template.html +share/EMBOSS/jemboss/utils/README +share/EMBOSS/jemboss/LICENSE +share/EMBOSS/jemboss/readme.html +share/EMBOSS/jemboss/runJemboss.sh +share/EMBOSS/jemboss/README +%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals +%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html +%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text +%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs +%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials +%%PORTDOCS%%@dirrm %%DOCSDIR%% +@dirrm share/EMBOSS/acd +@dirrm share/EMBOSS/data/AAINDEX +@dirrm share/EMBOSS/data/CODONS +@dirrm share/EMBOSS/data/REBASE +@dirrm share/EMBOSS/data/PRINTS +@dirrm share/EMBOSS/data/PROSITE +@dirrm share/EMBOSS/data +@dirrm share/EMBOSS/test/data +@dirrm share/EMBOSS/test/embl @dirrm share/EMBOSS/test/genbank @dirrm share/EMBOSS/test/gb -@dirrm share/EMBOSS/test/embl -@dirrm share/EMBOSS/test/data +@dirrm share/EMBOSS/test/pir +@dirrm share/EMBOSS/test/swiss +@dirrm share/EMBOSS/test/swnew +@dirrm share/EMBOSS/test/wormpep @dirrm share/EMBOSS/test -@dirrm share/EMBOSS/jemboss/utils -@dirrm share/EMBOSS/jemboss/resources -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/soap -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/server -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/programs -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/startup -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/sequenceChooser -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/form -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui -@dirrm share/EMBOSS/jemboss/org/emboss/jemboss -@dirrm share/EMBOSS/jemboss/org/emboss -@dirrm share/EMBOSS/jemboss/org -@dirrm share/EMBOSS/jemboss/lib -@dirrm share/EMBOSS/jemboss/images -@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/soap -@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/programs -@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd -@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser -@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/startup -@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/sequenceChooser -@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/filetree +@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form +@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/sequenceChooser +@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/startup @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/gui +@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd +@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser +@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/programs +@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/soap @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss @dirrm share/EMBOSS/jemboss/api/org/emboss @dirrm share/EMBOSS/jemboss/api/org @dirrm share/EMBOSS/jemboss/api +@dirrm share/EMBOSS/jemboss/images +@dirrm share/EMBOSS/jemboss/lib/axis +@dirrm share/EMBOSS/jemboss/lib +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/editor +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/draw +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/form +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/sequenceChooser +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/startup +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/parser +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/programs +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/server +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/soap +@dirrm share/EMBOSS/jemboss/org/emboss/jemboss +@dirrm share/EMBOSS/jemboss/org/emboss +@dirrm share/EMBOSS/jemboss/org +@dirrm share/EMBOSS/jemboss/resources +@dirrm share/EMBOSS/jemboss/utils @dirrm share/EMBOSS/jemboss -@dirrm share/EMBOSS/data/REBASE -@dirrm share/EMBOSS/data/PROSITE -@dirrm share/EMBOSS/data/PRINTS -@dirrm share/EMBOSS/data/CODONS -@dirrm share/EMBOSS/data -@dirrm share/EMBOSS/acd @dirrm share/EMBOSS diff -ruN /usr/ports/biology/emboss/scripts/configure.emboss emboss/scripts/configure.emboss --- /usr/ports/biology/emboss/scripts/configure.emboss Fri Aug 3 08:32:42 2001 +++ emboss/scripts/configure.emboss Wed Dec 31 21:00:00 1969 @@ -1,73 +0,0 @@ -#!/bin/sh - -if [ -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc ]; then - exit -fi - -if [ "${BATCH}" ]; then - set \"EMNU\" \"HMMER\" \"MEME\" \"MSE\" \"PHYLIP\" \"TOPO\" -else - /usr/bin/dialog --title "EMBOSS: EMBASSY applications" --clear \ - --checklist "\n\ -These third party applications have been adapted to -function as part of EMBOSS.\n -Please select EMBASSY applications to install:" -1 -1 6 \ -EMNU "v${EMNU_VERSION} - Text-based menu" ON \ -HMMER "v${HMMER_VERSION} - HMM alignment" ON \ -MEME "v${MEME_VERSION} - Motif detection" ON \ -MSE "v${MSE_VERSION} - Phylogeny inference" ON \ -PHYLIP "v${PHYLIP_VERSION} - Sequence editor" ON \ -TOPO "v${TOPO_VERSION} - Transmembrane display" ON \ -2> /tmp/checklist.tmp.$$ - - retval=$? - - if [ -s /tmp/checklist.tmp.$$ ]; then - set `cat /tmp/checklist.tmp.$$` - fi - ${RM} -f /tmp/checklist.tmp.$$ - - case $retval in - 0) - if [ -z "$*" ]; then - echo "Nothing selected" - fi - ;; - 1) - echo "Cancel pressed." - exit 1 - ;; - esac -fi - -${MKDIR} ${WRKDIRPREFIX}${CURDIR} -exec > ${WRKDIRPREFIX}${CURDIR}/Makefile.inc - -while [ "$1" ]; do - case $1 in - \"EMNU\") - echo "WITH_EMNU= yes" - ;; - \"HMMER\") - echo "WITH_HMMER= yes" - ;; - \"MEME\") - echo "WITH_MEME= yes" - ;; - \"MSE\") - echo "WITH_MSE= yes" - ;; - \"PHYLIP\") - echo "WITH_PHYLIP= yes" - ;; - \"TOPO\") - echo "WITH_TOPO= yes" - ;; - *) - echo "Invalid option(s): $*" > /dev/stderr - ${RM} -f ${WRKDIRPREFIX}${CURDIR}/Makefile.inc - exit 1 - ;; - esac - shift -done --- emboss.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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